2010  #startprog                                      
2020  # EndProj                                      
1  #  q                                    
0.23  #  M Immature   female                                  
0.23  #  M Immature   Male                                  
0.23  #  Mature newshell M  female                                  
0.23  #  Mature newshell M  Male                                  
0.23  #  Mature old shell M  female                                  
0.23  #  Mature old shell M  Male                                  
-1  #  molting  prob  mature  male  phase  (set  to  -1  for  terminal  molt)                
-1  #  phase  for  estimating  dome  shaped  fishery  selectivity  parameters  (-1  for  no  dome  shpaed)            
1  #growth  switch  males  1  for  st.  marie  2  for  st.marie  then  same  after  90mm            
4  #phase  to  estimate  1989  to  present  period  survey  selectivity(set  to  4)  if  negative  then  fixed  at  Somerton  and  Otto  
4  #phase  to  estimate  1978  to  1982  and  1983-1988  survey  selectivity(set  to  4)  if  negative  then  fixed  at  Somerton  and  Otto
9  #phase  to  estimate  future  projections                              
692528  #median  rec  for  last  year                              
542191  #median  rec  for  future  years                              
0  #number  of  years  to  fix  recruits                            
32  #number  of  length  bins  female                              
32  #number  of  length  bins  male                              
1  #switch  for  smooth  selectivity  fishery                              
1  #switch  for  smooth  selectivity  survey                              
3  #phase  for  estimating  fishery  and  bycatch  selectivity  curves                        
-1  #phase  for  estimating  smooth  selectivities                              
#parameters  for  somerton  selectivity  curve  (not  standard  logistic)                          
#underbag  experiment                                      
#0.9894                                        
#14.49                                        
#0.0366                                        
#somerton  report  2009  industry  survey  108  tows                            
#  model:  rat.m  ~  a/(1  +  exp(-(b  +  c  *  width.m)))                    
#  a  b  c                                  
#  0.8418  -2.6466  0.0354                                  
0.8418                                        
-2.6466                                        
0.0354                                        
7.905                                        
0.081                                        
#weights  for  smooth  sel  -  not  used                            
  10                                      
  40                                      
  40                                      
  40                                      
#  second  number  is  weight  for  retained  catch  -  multiplied  by  10*  in  later  phases            
  2000                                      
  1000                                      
  100000                                      
  10000                                      
#next  eight  values  are  like_wght(i),  1  to  8                          
1  #  weight  for  retained  length  comps                            
1  #weight  tot  length  comps                                
1  #weight  for  female  pot  fishery  discard  length  comps                        
1  #weight  for  survey  length  comps                              
1  #survey  biomass  cv  factor  multiplied  times  the  obs  cv's  female                    
50  #  weight  for  retained  catch  biomass                            
1  #weight  for  trawl  bycatch  length  comps                            
1  #survey  biomass  cv  factor  multiplied  times  the  obs  cv's  #male                    
0.001  #weight  for  male  recruitment  devs                              
0.001  #weight  for  female  rec  devs                              
0.001  #weight  for  sex  ratio                                
100  #weight  for  fishery  50%  selectivity  deviations                            
10  #weight  for  fmorts  pot  fishery  phase  1                          
2  #weight  for  fmorts  pot  fishery  after  phase  1                        
0.1  #weight  for  fmort  deviations  pot  fishery                            
0.5  #assumed  mortality  for  pot  fishery  bycatch                            
0.8  #mortality  for  trawl  bycatch                                
#growth  parameters  from  ST.  Marie  with  sd(for  priors  not  estimated)                      
5.9417                                        
0.59                                        
6.0652                                        
0.5                                        
1.1067                                        
0.25                                        
1.1238                                        
0.25                                        
#not  used  above  here                                  
#prior  means  followed  by  sd  for  growth  parameters                          
#these  are  the  parameters  used  in  model                            
  2.683    #female  a  <95                                    
17.75      #female  >95                                      
0.001      #sd  a                                      
3.87       #male  a   crab  <=100                                      
15.75      #crab  >100                                      
0.01       #sd  a                                      
1.221      #female  b                                      
1.07                                        
0.0001     #sd  b                                      
1.186      #male  b  crab  <  105                                    
#  males  >  105                                  
1.07  #  this  gives  approx  same  growth  with  intercept  at  6.773  same  for  males  and  females          
0.001 #sd  b                                      
3.6   #sd  at  recruitment                                    
0.1                                        
10.5 #sd  at  max  length                                  
0.2  
1.72 #mating  ratio  for  estimation  of  effective  spawning  biomass                          
1    #fraction  of  new  shell  animals  that  are  0<1  yr  from  molting  (error  in  shell  condition)            
2    #if greater  than  0  then  use  maturity  logistic  curve  instead  of  fractions  by  year  for  probability  of  new  shell  maturity  
10   #number  of  ages  to  track  for  old  shell  mature  animals                      
#weight  for  total  (retained  plus  discard)  catch  likelihood                          
#weight  increases  in  last  phases  by  10*  to  fit  catch  closely  otherwise  problems                
#in  converging  at  earlier  stages                                
10  #weight  used  to  fit  discards                              
10  #weight  for  female  pot  bycatch  likelihood                            
5  #CV  for  the  fit  to  pot  fishery  likelihood  -  larger  means  less  weight  on  fit          
0.001  #wt  for  fitting  large  male  (>101)  survey  numbers  at  later  phases  this  increased  by  2.0*                            
#______________________________________________
0    # Q prior switch (0=don't use, 1=use)
1    # killem switch  (0=don't use, 1=use)
2    # n_qs Number of survey q periods (both female and male
1974 1982 # year(s) of change in q (numbers n_qs - 1)
#  matestf = 
  -14.9999992180 -13.5855305973 -12.1281449222 -10.5849267233 -8.91324393852 -7.07400495920 -5.05548198024 -2.98137278741 -1.49108752486 -0.598844186143 -0.214010234393 -0.0204652242147 -9.39035516012e-011 -4.23892032586e-011 -3.47455397787e-011 -3.85664833402e-011
#  matestm = 
  -14.9999980402 -13.8199734692 -12.6068599350 -11.3275729738 -9.94947452544 -8.44406295444 -6.81007555868 -5.17528919339 -4.24849229332 -3.64989652976 -3.02680671285 -2.43738984872 -2.01353897942 -1.60011372087 -1.28524248666 -1.08085259822 -0.810809178777 -0.457375046987 -0.207915369246 -0.0801438865440 -0.0183885493331 -8.42160119419e-010 -4.30109281524e-010 -3.12493142474e-010 -3.51707996060e-010 -4.27951007964e-010 -6.25089313644e-010 -1.08678754884e-009 -2.49781528794e-009 -9.21767373541e-009 -8.35257587539e-008 -0.000256804625796
# End of controle file
123456789
